HTSMultiQC-cleaning-report
A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2022-01-03, 17:42
based on data in:
/share/dandekarlab/Houston/SCRI_Root_RNAseq_work/01-HTS_Preproc
HTStream
HTStream quality control and processing pipeline for High Throughput Sequencing data.
hts_Stats
Generates a JSON formatted file containing a set of statistical measures about the input read data.
| Sample Name | % PE | % R1 Q30 | % R2 Q30 | GC Content | N Content | Notes |
|---|---|---|---|---|---|---|
| 29JM-11-1 | 100.00% | 89.95% | 86.19% | 48.78% | 0.0000% | initial stats |
| 29JM-11-2 | 100.00% | 86.87% | 84.50% | 50.27% | 0.0000% | initial stats |
| 29JM-11-3 | 100.00% | 89.06% | 86.00% | 48.08% | 0.0000% | initial stats |
| 29JM-11-4 | 100.00% | 89.58% | 86.71% | 47.69% | 0.0000% | initial stats |
| 29JM-11-5 | 100.00% | 89.44% | 86.47% | 48.44% | 0.0000% | initial stats |
| 29JM-11-6 | 100.00% | 90.53% | 86.97% | 46.47% | 0.0000% | initial stats |
| JMS-12-1 | 100.00% | 90.14% | 86.46% | 46.18% | 0.0000% | initial stats |
| JMS-12-2 | 100.00% | 90.18% | 86.28% | 46.62% | 0.0000% | initial stats |
| JMS-12-3 | 100.00% | 90.60% | 86.83% | 46.27% | 0.0000% | initial stats |
| JMS-12-4 | 100.00% | 89.14% | 86.58% | 48.52% | 0.0000% | initial stats |
| JMS-12-5 | 100.00% | 90.15% | 86.38% | 46.36% | 0.0000% | initial stats |
| JMS-12-6 | 100.00% | 90.36% | 86.67% | 46.17% | 0.0000% | initial stats |
| MS1-122-1 | 100.00% | 89.93% | 84.79% | 45.76% | 0.0000% | initial stats |
| MS1-122-2 | 100.00% | 89.44% | 86.22% | 46.30% | 0.0000% | initial stats |
| MS1-122-3 | 100.00% | 89.34% | 83.76% | 46.41% | 0.0000% | initial stats |
| MS1-122-4 | 100.00% | 89.14% | 84.43% | 47.69% | 0.0000% | initial stats |
| MS1-122-5 | 100.00% | 89.41% | 85.95% | 46.18% | 0.0000% | initial stats |
| MS1-122-6 | 100.00% | 89.58% | 86.75% | 47.98% | 0.0000% | initial stats |
| MS1-36-1 | 100.00% | 89.76% | 85.56% | 46.47% | 0.0000% | initial stats |
| MS1-36-2 | 100.00% | 89.54% | 82.48% | 46.62% | 0.0000% | initial stats |
| MS1-36-3 | 100.00% | 90.71% | 85.49% | 45.79% | 0.0000% | initial stats |
| MS1-36-4 | 100.00% | 90.80% | 87.34% | 46.18% | 0.0000% | initial stats |
| MS1-36-5 | 100.00% | 88.71% | 83.98% | 47.56% | 0.0000% | initial stats |
| MS1-36-6 | 100.00% | 90.71% | 86.18% | 47.12% | 0.0000% | initial stats |
| MS1-41-1 | 100.00% | 89.81% | 86.50% | 46.46% | 0.0000% | initial stats |
| MS1-41-2 | 100.00% | 88.67% | 85.74% | 49.03% | 0.0000% | initial stats |
| MS1-41-3 | 100.00% | 90.09% | 85.91% | 46.46% | 0.0000% | initial stats |
| MS1-41-4 | 100.00% | 89.72% | 85.65% | 46.91% | 0.0000% | initial stats |
| MS1-41-5 | 100.00% | 89.73% | 86.31% | 49.19% | 0.0000% | initial stats |
| MS1-41-6 | 100.00% | 89.41% | 85.96% | 47.14% | 0.0000% | initial stats |
| MS1-56-1 | 100.00% | 89.40% | 86.18% | 46.52% | 0.0000% | initial stats |
| MS1-56-2 | 100.00% | 89.40% | 85.97% | 47.35% | 0.0000% | initial stats |
| MS1-56-3 | 100.00% | 89.78% | 86.63% | 47.04% | 0.0000% | initial stats |
| MS1-56-4 | 100.00% | 90.23% | 87.04% | 47.05% | 0.0000% | initial stats |
| MS1-56-5 | 100.00% | 89.01% | 86.58% | 51.90% | 0.0000% | initial stats |
| MS1-56-6 | 100.00% | 90.49% | 87.13% | 47.99% | 0.0000% | initial stats |
| STJM-4-1 | 100.00% | 86.14% | 85.65% | 52.02% | 0.0000% | initial stats |
| STJM-4-2 | 100.00% | 88.29% | 86.19% | 47.83% | 0.0000% | initial stats |
| STJM-4-3 | 100.00% | 88.24% | 85.31% | 46.71% | 0.0000% | initial stats |
| STJM-4-4 | 100.00% | 89.92% | 86.18% | 47.84% | 0.0000% | initial stats |
| STJM-4-5 | 100.00% | 87.84% | 85.25% | 48.26% | 0.0000% | initial stats |
| STJM-4-6 | 100.00% | 89.11% | 85.65% | 48.27% | 0.0000% | initial stats |
Read Lengths: Paired End
Distribution of read lengths for each sample.
Notice: Each sample has a uniform read length distribution.
Showing 42/42 rows and 2/2 columns.
| Sample Name | R1 Read Lengths | R2 Read Lengths |
|---|---|---|
| 29JM-11-1 | 151 | 151 |
| 29JM-11-2 | 151 | 151 |
| 29JM-11-3 | 151 | 151 |
| 29JM-11-4 | 151 | 151 |
| 29JM-11-5 | 151 | 151 |
| 29JM-11-6 | 151 | 151 |
| JMS-12-1 | 151 | 151 |
| JMS-12-2 | 151 | 151 |
| JMS-12-3 | 151 | 151 |
| JMS-12-4 | 151 | 151 |
| JMS-12-5 | 151 | 151 |
| JMS-12-6 | 151 | 151 |
| MS1-122-1 | 151 | 151 |
| MS1-122-2 | 151 | 151 |
| MS1-122-3 | 151 | 151 |
| MS1-122-4 | 151 | 151 |
| MS1-122-5 | 151 | 151 |
| MS1-122-6 | 151 | 151 |
| MS1-36-1 | 151 | 151 |
| MS1-36-2 | 151 | 151 |
| MS1-36-3 | 151 | 151 |
| MS1-36-4 | 151 | 151 |
| MS1-36-5 | 151 | 151 |
| MS1-36-6 | 151 | 151 |
| MS1-41-1 | 151 | 151 |
| MS1-41-2 | 151 | 151 |
| MS1-41-3 | 151 | 151 |
| MS1-41-4 | 151 | 151 |
| MS1-41-5 | 151 | 151 |
| MS1-41-6 | 151 | 151 |
| MS1-56-1 | 151 | 151 |
| MS1-56-2 | 151 | 151 |
| MS1-56-3 | 151 | 151 |
| MS1-56-4 | 151 | 151 |
| MS1-56-5 | 151 | 151 |
| MS1-56-6 | 151 | 151 |
| STJM-4-1 | 151 | 151 |
| STJM-4-2 | 151 | 151 |
| STJM-4-3 | 151 | 151 |
| STJM-4-4 | 151 | 151 |
| STJM-4-5 | 151 | 151 |
| STJM-4-6 | 151 | 151 |
Base by Cycle: Paired End
Provides a measure of the uniformity of a distribution. The higher the average is at a certain position, the more unequal the base pair composition. N's are excluded from this calculation.
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Quality by Cycle: Paired End
Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.
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hts_SeqScreener
A simple sequence screening tool which uses a kmer lookup approach to identify reads from an unwanted source.
| Sample Name | PE hits | % PE Hits | Notes |
|---|---|---|---|
| 29JM-11-1 | 1 | 0.0000% | screen phix |
| 29JM-11-2 | 0 | 0.0000% | screen phix |
| 29JM-11-3 | 0 | 0.0000% | screen phix |
| 29JM-11-4 | 0 | 0.0000% | screen phix |
| 29JM-11-5 | 0 | 0.0000% | screen phix |
| 29JM-11-6 | 0 | 0.0000% | screen phix |
| JMS-12-1 | 0 | 0.0000% | screen phix |
| JMS-12-2 | 2 | 0.0000% | screen phix |
| JMS-12-3 | 0 | 0.0000% | screen phix |
| JMS-12-4 | 1 | 0.0000% | screen phix |
| JMS-12-5 | 3 | 0.0000% | screen phix |
| JMS-12-6 | 1 | 0.0000% | screen phix |
| MS1-122-1 | 0 | 0.0000% | screen phix |
| MS1-122-2 | 0 | 0.0000% | screen phix |
| MS1-122-3 | 0 | 0.0000% | screen phix |
| MS1-122-4 | 0 | 0.0000% | screen phix |
| MS1-122-5 | 0 | 0.0000% | screen phix |
| MS1-122-6 | 2 | 0.0000% | screen phix |
| MS1-36-1 | 0 | 0.0000% | screen phix |
| MS1-36-2 | 0 | 0.0000% | screen phix |
| MS1-36-3 | 0 | 0.0000% | screen phix |
| MS1-36-4 | 1 | 0.0000% | screen phix |
| MS1-36-5 | 0 | 0.0000% | screen phix |
| MS1-36-6 | 0 | 0.0000% | screen phix |
| MS1-41-1 | 0 | 0.0000% | screen phix |
| MS1-41-2 | 0 | 0.0000% | screen phix |
| MS1-41-3 | 0 | 0.0000% | screen phix |
| MS1-41-4 | 0 | 0.0000% | screen phix |
| MS1-41-5 | 0 | 0.0000% | screen phix |
| MS1-41-6 | 1 | 0.0000% | screen phix |
| MS1-56-1 | 0 | 0.0000% | screen phix |
| MS1-56-2 | 0 | 0.0000% | screen phix |
| MS1-56-3 | 0 | 0.0000% | screen phix |
| MS1-56-4 | 2 | 0.0000% | screen phix |
| MS1-56-5 | 1 | 0.0000% | screen phix |
| MS1-56-6 | 1 | 0.0000% | screen phix |
| STJM-4-1 | 0 | 0.0000% | screen phix |
| STJM-4-2 | 1 | 0.0000% | screen phix |
| STJM-4-3 | 0 | 0.0000% | screen phix |
| STJM-4-4 | 3 | 0.0000% | screen phix |
| STJM-4-5 | 0 | 0.0000% | screen phix |
| STJM-4-6 | 0 | 0.0000% | screen phix |
hts_SeqScreener 2
A simple sequence screening tool which uses a kmer lookup approach to identify reads from an unwanted source.
| Sample Name | PE hits | % PE Hits | Notes |
|---|---|---|---|
| 29JM-11-1 | 3093995 | 21.6919% | count the number of rRNA reads |
| 29JM-11-2 | 4061581 | 41.7823% | count the number of rRNA reads |
| 29JM-11-3 | 2926056 | 24.6395% | count the number of rRNA reads |
| 29JM-11-4 | 3746781 | 20.0501% | count the number of rRNA reads |
| 29JM-11-5 | 4634312 | 27.0060% | count the number of rRNA reads |
| 29JM-11-6 | 239295 | 1.1400% | count the number of rRNA reads |
| JMS-12-1 | 172648 | 1.2984% | count the number of rRNA reads |
| JMS-12-2 | 547911 | 4.9555% | count the number of rRNA reads |
| JMS-12-3 | 808672 | 5.1465% | count the number of rRNA reads |
| JMS-12-4 | 3004810 | 27.8810% | count the number of rRNA reads |
| JMS-12-5 | 692571 | 4.4940% | count the number of rRNA reads |
| JMS-12-6 | 230864 | 1.6761% | count the number of rRNA reads |
| MS1-122-1 | 138010 | 1.2019% | count the number of rRNA reads |
| MS1-122-2 | 548745 | 3.4746% | count the number of rRNA reads |
| MS1-122-3 | 505136 | 3.1594% | count the number of rRNA reads |
| MS1-122-4 | 2801765 | 15.7665% | count the number of rRNA reads |
| MS1-122-5 | 719335 | 3.8210% | count the number of rRNA reads |
| MS1-122-6 | 4411886 | 22.8508% | count the number of rRNA reads |
| MS1-36-1 | 642047 | 3.0498% | count the number of rRNA reads |
| MS1-36-2 | 1477544 | 6.3310% | count the number of rRNA reads |
| MS1-36-3 | 328659 | 1.5200% | count the number of rRNA reads |
| MS1-36-4 | 339714 | 2.6586% | count the number of rRNA reads |
| MS1-36-5 | 1614528 | 11.6100% | count the number of rRNA reads |
| MS1-36-6 | 2975559 | 11.1945% | count the number of rRNA reads |
| MS1-41-1 | 2602501 | 13.4520% | count the number of rRNA reads |
| MS1-41-2 | 3546070 | 27.8019% | count the number of rRNA reads |
| MS1-41-3 | 314666 | 2.9254% | count the number of rRNA reads |
| MS1-41-4 | 395811 | 4.0205% | count the number of rRNA reads |
| MS1-41-5 | 5689857 | 24.8027% | count the number of rRNA reads |
| MS1-41-6 | 1580991 | 10.0976% | count the number of rRNA reads |
| MS1-56-1 | 474936 | 2.6893% | count the number of rRNA reads |
| MS1-56-2 | 1401384 | 8.1975% | count the number of rRNA reads |
| MS1-56-3 | 953551 | 5.8386% | count the number of rRNA reads |
| MS1-56-4 | 866827 | 7.1640% | count the number of rRNA reads |
| MS1-56-5 | 8185566 | 62.0490% | count the number of rRNA reads |
| MS1-56-6 | 3294702 | 13.4853% | count the number of rRNA reads |
| STJM-4-1 | 6421285 | 61.4649% | count the number of rRNA reads |
| STJM-4-2 | 672639 | 4.2700% | count the number of rRNA reads |
| STJM-4-3 | 190321 | 1.9589% | count the number of rRNA reads |
| STJM-4-4 | 1009984 | 7.9049% | count the number of rRNA reads |
| STJM-4-5 | 1374979 | 10.2073% | count the number of rRNA reads |
| STJM-4-6 | 1763251 | 16.5958% | count the number of rRNA reads |
hts_SuperDeduper
A reference free duplicate read removal tool.
| Sample Name | % Duplicates | % Ignored | Notes |
|---|---|---|---|
| 29JM-11-1 | 76.94% | 0.00% | remove PCR duplicates |
| 29JM-11-2 | 88.32% | 0.00% | remove PCR duplicates |
| 29JM-11-3 | 68.00% | 0.00% | remove PCR duplicates |
| 29JM-11-4 | 65.30% | 0.00% | remove PCR duplicates |
| 29JM-11-5 | 55.68% | 0.00% | remove PCR duplicates |
| 29JM-11-6 | 58.92% | 0.00% | remove PCR duplicates |
| JMS-12-1 | 57.40% | 0.00% | remove PCR duplicates |
| JMS-12-2 | 52.06% | 0.00% | remove PCR duplicates |
| JMS-12-3 | 57.80% | 0.00% | remove PCR duplicates |
| JMS-12-4 | 52.85% | 0.00% | remove PCR duplicates |
| JMS-12-5 | 56.14% | 0.00% | remove PCR duplicates |
| JMS-12-6 | 39.00% | 0.00% | remove PCR duplicates |
| MS1-122-1 | 50.35% | 0.00% | remove PCR duplicates |
| MS1-122-2 | 50.99% | 0.00% | remove PCR duplicates |
| MS1-122-3 | 48.44% | 0.00% | remove PCR duplicates |
| MS1-122-4 | 72.74% | 0.00% | remove PCR duplicates |
| MS1-122-5 | 40.25% | 0.00% | remove PCR duplicates |
| MS1-122-6 | 73.14% | 0.00% | remove PCR duplicates |
| MS1-36-1 | 57.28% | 0.00% | remove PCR duplicates |
| MS1-36-2 | 72.32% | 0.00% | remove PCR duplicates |
| MS1-36-3 | 34.10% | 0.00% | remove PCR duplicates |
| MS1-36-4 | 46.29% | 0.00% | remove PCR duplicates |
| MS1-36-5 | 64.75% | 0.00% | remove PCR duplicates |
| MS1-36-6 | 65.12% | 0.00% | remove PCR duplicates |
| MS1-41-1 | 62.24% | 0.00% | remove PCR duplicates |
| MS1-41-2 | 66.74% | 0.00% | remove PCR duplicates |
| MS1-41-3 | 45.55% | 0.00% | remove PCR duplicates |
| MS1-41-4 | 45.78% | 0.00% | remove PCR duplicates |
| MS1-41-5 | 67.23% | 0.00% | remove PCR duplicates |
| MS1-41-6 | 62.07% | 0.00% | remove PCR duplicates |
| MS1-56-1 | 59.95% | 0.00% | remove PCR duplicates |
| MS1-56-2 | 61.34% | 0.00% | remove PCR duplicates |
| MS1-56-3 | 57.05% | 0.00% | remove PCR duplicates |
| MS1-56-4 | 54.76% | 0.00% | remove PCR duplicates |
| MS1-56-5 | 79.39% | 0.00% | remove PCR duplicates |
| MS1-56-6 | 62.21% | 0.00% | remove PCR duplicates |
| STJM-4-1 | 89.31% | 0.00% | remove PCR duplicates |
| STJM-4-2 | 81.81% | 0.00% | remove PCR duplicates |
| STJM-4-3 | 83.16% | 0.00% | remove PCR duplicates |
| STJM-4-4 | 69.37% | 0.00% | remove PCR duplicates |
| STJM-4-5 | 85.72% | 0.00% | remove PCR duplicates |
| STJM-4-6 | 78.60% | 0.00% | remove PCR duplicates |
SuperDeduper: Duplicate Saturation
Plots the number of duplicates against the number of unique reads per sample.
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hts_AdapterTrimmer
Trims adapters which are sequenced when the fragment insert length is shorter than the read length.
| Sample Name | % Bp Lost | % Adapters | Avg. Bps Trimmed | Notes |
|---|---|---|---|---|
| 29JM-11-1 | 4.99% | 44.71% | 33.67 | trim adapters |
| 29JM-11-2 | 1.92% | 17.47% | 33.10 | trim adapters |
| 29JM-11-3 | 5.35% | 46.86% | 34.47 | trim adapters |
| 29JM-11-4 | 4.87% | 43.24% | 34.02 | trim adapters |
| 29JM-11-5 | 4.89% | 44.18% | 33.41 | trim adapters |
| 29JM-11-6 | 4.57% | 42.20% | 32.69 | trim adapters |
| JMS-12-1 | 5.31% | 47.35% | 33.85 | trim adapters |
| JMS-12-2 | 3.83% | 37.89% | 30.50 | trim adapters |
| JMS-12-3 | 5.58% | 51.62% | 32.65 | trim adapters |
| JMS-12-4 | 6.82% | 60.13% | 34.28 | trim adapters |
| JMS-12-5 | 5.65% | 52.14% | 32.74 | trim adapters |
| JMS-12-6 | 3.85% | 34.85% | 33.35 | trim adapters |
| MS1-122-1 | 5.35% | 47.52% | 34.01 | trim adapters |
| MS1-122-2 | 3.95% | 35.16% | 33.94 | trim adapters |
| MS1-122-3 | 3.01% | 27.39% | 33.14 | trim adapters |
| MS1-122-4 | 3.73% | 33.25% | 33.85 | trim adapters |
| MS1-122-5 | 3.43% | 30.58% | 33.88 | trim adapters |
| MS1-122-6 | 4.29% | 39.96% | 32.39 | trim adapters |
| MS1-36-1 | 3.07% | 30.08% | 30.82 | trim adapters |
| MS1-36-2 | 4.01% | 37.71% | 32.15 | trim adapters |
| MS1-36-3 | 4.08% | 37.45% | 32.94 | trim adapters |
| MS1-36-4 | 6.61% | 59.95% | 33.32 | trim adapters |
| MS1-36-5 | 2.92% | 27.10% | 32.53 | trim adapters |
| MS1-36-6 | 3.61% | 31.80% | 34.29 | trim adapters |
| MS1-41-1 | 5.61% | 49.56% | 34.20 | trim adapters |
| MS1-41-2 | 4.68% | 41.18% | 34.29 | trim adapters |
| MS1-41-3 | 4.39% | 40.28% | 32.90 | trim adapters |
| MS1-41-4 | 4.24% | 37.93% | 33.72 | trim adapters |
| MS1-41-5 | 4.09% | 36.70% | 33.69 | trim adapters |
| MS1-41-6 | 4.01% | 35.78% | 33.82 | trim adapters |
| MS1-56-1 | 3.16% | 30.22% | 31.62 | trim adapters |
| MS1-56-2 | 3.65% | 34.03% | 32.41 | trim adapters |
| MS1-56-3 | 4.63% | 42.25% | 33.10 | trim adapters |
| MS1-56-4 | 5.11% | 48.52% | 31.79 | trim adapters |
| MS1-56-5 | 4.00% | 36.64% | 33.01 | trim adapters |
| MS1-56-6 | 4.09% | 38.09% | 32.40 | trim adapters |
| STJM-4-1 | 2.32% | 21.79% | 32.22 | trim adapters |
| STJM-4-2 | 3.28% | 29.96% | 33.09 | trim adapters |
| STJM-4-3 | 2.57% | 24.14% | 32.12 | trim adapters |
| STJM-4-4 | 3.58% | 32.58% | 33.16 | trim adapters |
| STJM-4-5 | 3.25% | 30.31% | 32.40 | trim adapters |
| STJM-4-6 | 4.05% | 37.18% | 32.86 | trim adapters |
AdapterTrimmer: Trimmed Basepairs Composition
Composition of basepairs trimmed from the ends of paired end and single end reads.
hts_PolyATTrim
Attempts to trim poly-A and poly-T sequences from the end of reads.
| Sample Name | Total Bp Lost | % R1 of Bp Lost | % R2 of Bp Lost | Notes |
|---|---|---|---|---|
| 29JM-11-1 | 25189 | 0.00% | 100.00% | remove polyAT tails |
| 29JM-11-2 | 11035 | 0.00% | 100.00% | remove polyAT tails |
| 29JM-11-3 | 40364 | 0.00% | 100.00% | remove polyAT tails |
| 29JM-11-4 | 76357 | 0.00% | 100.00% | remove polyAT tails |
| 29JM-11-5 | 85171 | 0.00% | 100.00% | remove polyAT tails |
| 29JM-11-6 | 100950 | 0.00% | 100.00% | remove polyAT tails |
| JMS-12-1 | 67682 | 0.00% | 100.00% | remove polyAT tails |
| JMS-12-2 | 61972 | 0.00% | 100.00% | remove polyAT tails |
| JMS-12-3 | 84637 | 0.00% | 100.00% | remove polyAT tails |
| JMS-12-4 | 65092 | 0.00% | 100.00% | remove polyAT tails |
| JMS-12-5 | 88380 | 0.00% | 100.00% | remove polyAT tails |
| JMS-12-6 | 106881 | 0.00% | 100.00% | remove polyAT tails |
| MS1-122-1 | 56933 | 0.00% | 100.00% | remove polyAT tails |
| MS1-122-2 | 79320 | 0.00% | 100.00% | remove polyAT tails |
| MS1-122-3 | 90020 | 0.00% | 100.00% | remove polyAT tails |
| MS1-122-4 | 42163 | 0.00% | 100.00% | remove polyAT tails |
| MS1-122-5 | 120556 | 0.00% | 100.00% | remove polyAT tails |
| MS1-122-6 | 52842 | 0.00% | 100.00% | remove polyAT tails |
| MS1-36-1 | 112492 | 0.00% | 100.00% | remove polyAT tails |
| MS1-36-2 | 79717 | 0.00% | 100.00% | remove polyAT tails |
| MS1-36-3 | 191250 | 0.00% | 100.00% | remove polyAT tails |
| MS1-36-4 | 81856 | 0.00% | 100.00% | remove polyAT tails |
| MS1-36-5 | 46937 | 0.00% | 100.00% | remove polyAT tails |
| MS1-36-6 | 81022 | 0.00% | 100.00% | remove polyAT tails |
| MS1-41-1 | 64490 | 0.00% | 100.00% | remove polyAT tails |
| MS1-41-2 | 34000 | 0.00% | 100.00% | remove polyAT tails |
| MS1-41-3 | 57790 | 0.00% | 100.00% | remove polyAT tails |
| MS1-41-4 | 54140 | 0.00% | 100.00% | remove polyAT tails |
| MS1-41-5 | 63013 | 0.00% | 100.00% | remove polyAT tails |
| MS1-41-6 | 57626 | 0.00% | 100.00% | remove polyAT tails |
| MS1-56-1 | 90586 | 0.00% | 100.00% | remove polyAT tails |
| MS1-56-2 | 78266 | 0.00% | 100.00% | remove polyAT tails |
| MS1-56-3 | 85127 | 0.00% | 100.00% | remove polyAT tails |
| MS1-56-4 | 58196 | 0.00% | 100.00% | remove polyAT tails |
| MS1-56-5 | 20103 | 0.00% | 100.00% | remove polyAT tails |
| MS1-56-6 | 99142 | 0.00% | 100.00% | remove polyAT tails |
| STJM-4-1 | 7725 | 0.00% | 100.00% | remove polyAT tails |
| STJM-4-2 | 29193 | 0.00% | 100.00% | remove polyAT tails |
| STJM-4-3 | 20113 | 0.00% | 100.00% | remove polyAT tails |
| STJM-4-4 | 41296 | 0.00% | 100.00% | remove polyAT tails |
| STJM-4-5 | 18833 | 0.00% | 100.00% | remove polyAT tails |
| STJM-4-6 | 22744 | 0.00% | 100.00% | remove polyAT tails |
hts_NTrimmer
Trims reads to the longest subsequence that contains no N's.
| Sample Name | Total Bp Lost | % R1 of Bp Lost | % R2 of Bp Lost | % Discarded | Notes |
|---|---|---|---|---|---|
| 29JM-11-1 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| 29JM-11-2 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| 29JM-11-3 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| 29JM-11-4 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| 29JM-11-5 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| 29JM-11-6 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| JMS-12-1 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| JMS-12-2 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| JMS-12-3 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| JMS-12-4 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| JMS-12-5 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| JMS-12-6 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-122-1 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-122-2 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-122-3 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-122-4 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-122-5 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-122-6 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-36-1 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-36-2 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-36-3 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-36-4 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-36-5 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-36-6 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-41-1 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-41-2 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-41-3 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-41-4 | -1 | -0.00% | 100.00% | 0.00% | remove any remaining N characters |
| MS1-41-5 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-41-6 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-56-1 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-56-2 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-56-3 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-56-4 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-56-5 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| MS1-56-6 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| STJM-4-1 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| STJM-4-2 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| STJM-4-3 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| STJM-4-4 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| STJM-4-5 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
| STJM-4-6 | 0 | 0.00% | 0.00% | 0.00% | remove any remaining N characters |
NTrimmer: Trimmed Basepairs Composition
Plots the number of N bases trimmed from ends of paired end and single end reads.
hts_QWindowTrim
Uses a sliding window approach to remove the low quality ends of reads.
| Sample Name | % Bp Lost | % R1 of Bp Lost | % R2 of Bp Lost | Avg. Bps Trimmed | Notes |
|---|---|---|---|---|---|
| 29JM-11-1 | 0.48% | 18.72% | 81.28% | 1.38 | quality trim the ends of reads |
| 29JM-11-2 | 0.69% | 18.70% | 81.30% | 2.03 | quality trim the ends of reads |
| 29JM-11-3 | 0.33% | 23.14% | 76.86% | 0.94 | quality trim the ends of reads |
| 29JM-11-4 | 0.22% | 31.36% | 68.64% | 0.63 | quality trim the ends of reads |
| 29JM-11-5 | 0.24% | 28.38% | 71.62% | 0.69 | quality trim the ends of reads |
| 29JM-11-6 | 0.23% | 30.91% | 69.09% | 0.65 | quality trim the ends of reads |
| JMS-12-1 | 0.25% | 26.21% | 73.79% | 0.72 | quality trim the ends of reads |
| JMS-12-2 | 0.27% | 26.39% | 73.61% | 0.78 | quality trim the ends of reads |
| JMS-12-3 | 0.24% | 28.49% | 71.51% | 0.70 | quality trim the ends of reads |
| JMS-12-4 | 0.24% | 27.58% | 72.42% | 0.69 | quality trim the ends of reads |
| JMS-12-5 | 0.25% | 27.58% | 72.42% | 0.72 | quality trim the ends of reads |
| JMS-12-6 | 0.20% | 34.01% | 65.99% | 0.57 | quality trim the ends of reads |
| MS1-122-1 | 0.33% | 21.48% | 78.52% | 0.94 | quality trim the ends of reads |
| MS1-122-2 | 0.20% | 32.66% | 67.34% | 0.58 | quality trim the ends of reads |
| MS1-122-3 | 0.20% | 31.14% | 68.86% | 0.60 | quality trim the ends of reads |
| MS1-122-4 | 0.28% | 27.82% | 72.18% | 0.83 | quality trim the ends of reads |
| MS1-122-5 | 0.19% | 34.34% | 65.66% | 0.54 | quality trim the ends of reads |
| MS1-122-6 | 0.28% | 30.06% | 69.94% | 0.81 | quality trim the ends of reads |
| MS1-36-1 | 0.24% | 30.07% | 69.93% | 0.70 | quality trim the ends of reads |
| MS1-36-2 | 0.32% | 28.01% | 71.99% | 0.93 | quality trim the ends of reads |
| MS1-36-3 | 0.22% | 31.88% | 68.12% | 0.63 | quality trim the ends of reads |
| MS1-36-4 | 0.24% | 25.23% | 74.77% | 0.69 | quality trim the ends of reads |
| MS1-36-5 | 0.25% | 31.41% | 68.59% | 0.73 | quality trim the ends of reads |
| MS1-36-6 | 0.29% | 26.46% | 73.54% | 0.85 | quality trim the ends of reads |
| MS1-41-1 | 0.25% | 31.08% | 68.92% | 0.72 | quality trim the ends of reads |
| MS1-41-2 | 0.32% | 24.78% | 75.22% | 0.93 | quality trim the ends of reads |
| MS1-41-3 | 0.27% | 25.50% | 74.50% | 0.79 | quality trim the ends of reads |
| MS1-41-4 | 0.25% | 26.88% | 73.12% | 0.72 | quality trim the ends of reads |
| MS1-41-5 | 0.27% | 28.21% | 71.79% | 0.79 | quality trim the ends of reads |
| MS1-41-6 | 0.27% | 27.84% | 72.16% | 0.79 | quality trim the ends of reads |
| MS1-56-1 | 0.27% | 30.69% | 69.31% | 0.78 | quality trim the ends of reads |
| MS1-56-2 | 0.25% | 32.78% | 67.22% | 0.71 | quality trim the ends of reads |
| MS1-56-3 | 0.23% | 30.84% | 69.16% | 0.67 | quality trim the ends of reads |
| MS1-56-4 | 0.24% | 27.01% | 72.99% | 0.68 | quality trim the ends of reads |
| MS1-56-5 | 0.38% | 27.69% | 72.31% | 1.11 | quality trim the ends of reads |
| MS1-56-6 | 0.25% | 31.93% | 68.07% | 0.74 | quality trim the ends of reads |
| STJM-4-1 | 0.65% | 22.38% | 77.62% | 1.91 | quality trim the ends of reads |
| STJM-4-2 | 0.32% | 29.61% | 70.39% | 0.93 | quality trim the ends of reads |
| STJM-4-3 | 0.53% | 18.56% | 81.44% | 1.55 | quality trim the ends of reads |
| STJM-4-4 | 0.26% | 27.98% | 72.02% | 0.77 | quality trim the ends of reads |
| STJM-4-5 | 0.52% | 21.66% | 78.34% | 1.53 | quality trim the ends of reads |
| STJM-4-6 | 0.48% | 19.27% | 80.73% | 1.38 | quality trim the ends of reads |
QWindowTrim: Trimmed Basepairs Composition
Plots the number of low quality basepairs trimmed from ends of paired end and single end reads.
hts_LengthFilter
Discards reads below a minimum length threshold.
| Sample Name | % PE Lost | Notes |
|---|---|---|
| 29JM-11-1 | 0.13% | remove reads < 50bp |
| 29JM-11-2 | 0.26% | remove reads < 50bp |
| 29JM-11-3 | 0.09% | remove reads < 50bp |
| 29JM-11-4 | 0.04% | remove reads < 50bp |
| 29JM-11-5 | 0.06% | remove reads < 50bp |
| 29JM-11-6 | 0.04% | remove reads < 50bp |
| JMS-12-1 | 0.06% | remove reads < 50bp |
| JMS-12-2 | 0.07% | remove reads < 50bp |
| JMS-12-3 | 0.05% | remove reads < 50bp |
| JMS-12-4 | 0.05% | remove reads < 50bp |
| JMS-12-5 | 0.06% | remove reads < 50bp |
| JMS-12-6 | 0.03% | remove reads < 50bp |
| MS1-122-1 | 0.12% | remove reads < 50bp |
| MS1-122-2 | 0.04% | remove reads < 50bp |
| MS1-122-3 | 0.04% | remove reads < 50bp |
| MS1-122-4 | 0.05% | remove reads < 50bp |
| MS1-122-5 | 0.03% | remove reads < 50bp |
| MS1-122-6 | 0.05% | remove reads < 50bp |
| MS1-36-1 | 0.05% | remove reads < 50bp |
| MS1-36-2 | 0.06% | remove reads < 50bp |
| MS1-36-3 | 0.04% | remove reads < 50bp |
| MS1-36-4 | 0.07% | remove reads < 50bp |
| MS1-36-5 | 0.05% | remove reads < 50bp |
| MS1-36-6 | 0.06% | remove reads < 50bp |
| MS1-41-1 | 0.05% | remove reads < 50bp |
| MS1-41-2 | 0.08% | remove reads < 50bp |
| MS1-41-3 | 0.07% | remove reads < 50bp |
| MS1-41-4 | 0.07% | remove reads < 50bp |
| MS1-41-5 | 0.05% | remove reads < 50bp |
| MS1-41-6 | 0.06% | remove reads < 50bp |
| MS1-56-1 | 0.05% | remove reads < 50bp |
| MS1-56-2 | 0.04% | remove reads < 50bp |
| MS1-56-3 | 0.05% | remove reads < 50bp |
| MS1-56-4 | 0.06% | remove reads < 50bp |
| MS1-56-5 | 0.06% | remove reads < 50bp |
| MS1-56-6 | 0.04% | remove reads < 50bp |
| STJM-4-1 | 0.15% | remove reads < 50bp |
| STJM-4-2 | 0.06% | remove reads < 50bp |
| STJM-4-3 | 0.18% | remove reads < 50bp |
| STJM-4-4 | 0.05% | remove reads < 50bp |
| STJM-4-5 | 0.17% | remove reads < 50bp |
| STJM-4-6 | 0.14% | remove reads < 50bp |
hts_Stats 2
Generates a JSON formatted file containing a set of statistical measures about the input read data.
| Sample Name | % PE | % R1 Q30 | % R2 Q30 | GC Content | N Content | Notes |
|---|---|---|---|---|---|---|
| 29JM-11-1 | 100.00% | 93.68% | 88.40% | 47.82% | 0.0000% | final stats |
| 29JM-11-2 | 100.00% | 90.32% | 84.23% | 48.40% | 0.0000% | final stats |
| 29JM-11-3 | 100.00% | 94.22% | 90.62% | 46.45% | 0.0000% | final stats |
| 29JM-11-4 | 100.00% | 94.65% | 91.86% | 46.20% | 0.0000% | final stats |
| 29JM-11-5 | 100.00% | 94.73% | 91.86% | 46.31% | 0.0000% | final stats |
| 29JM-11-6 | 100.00% | 95.01% | 91.84% | 46.48% | 0.0000% | final stats |
| JMS-12-1 | 100.00% | 94.99% | 91.86% | 45.83% | 0.0000% | final stats |
| JMS-12-2 | 100.00% | 94.83% | 91.57% | 46.36% | 0.0000% | final stats |
| JMS-12-3 | 100.00% | 95.16% | 91.95% | 46.01% | 0.0000% | final stats |
| JMS-12-4 | 100.00% | 95.35% | 92.19% | 45.74% | 0.0000% | final stats |
| JMS-12-5 | 100.00% | 95.06% | 92.00% | 45.77% | 0.0000% | final stats |
| JMS-12-6 | 100.00% | 94.68% | 91.91% | 45.85% | 0.0000% | final stats |
| MS1-122-1 | 100.00% | 94.77% | 90.76% | 45.34% | 0.0000% | final stats |
| MS1-122-2 | 100.00% | 94.45% | 91.89% | 45.83% | 0.0000% | final stats |
| MS1-122-3 | 100.00% | 94.22% | 90.27% | 45.95% | 0.0000% | final stats |
| MS1-122-4 | 100.00% | 93.46% | 89.40% | 47.12% | 0.0000% | final stats |
| MS1-122-5 | 100.00% | 94.19% | 91.57% | 45.65% | 0.0000% | final stats |
| MS1-122-6 | 100.00% | 94.13% | 90.67% | 46.96% | 0.0000% | final stats |
| MS1-36-1 | 100.00% | 94.38% | 90.77% | 46.02% | 0.0000% | final stats |
| MS1-36-2 | 100.00% | 93.73% | 88.40% | 46.49% | 0.0000% | final stats |
| MS1-36-3 | 100.00% | 94.72% | 90.91% | 45.28% | 0.0000% | final stats |
| MS1-36-4 | 100.00% | 95.72% | 92.84% | 45.43% | 0.0000% | final stats |
| MS1-36-5 | 100.00% | 93.82% | 89.88% | 46.52% | 0.0000% | final stats |
| MS1-36-6 | 100.00% | 93.91% | 89.79% | 46.32% | 0.0000% | final stats |
| MS1-41-1 | 100.00% | 94.78% | 91.22% | 46.08% | 0.0000% | final stats |
| MS1-41-2 | 100.00% | 94.07% | 90.30% | 47.47% | 0.0000% | final stats |
| MS1-41-3 | 100.00% | 94.68% | 91.18% | 46.14% | 0.0000% | final stats |
| MS1-41-4 | 100.00% | 94.50% | 91.29% | 46.55% | 0.0000% | final stats |
| MS1-41-5 | 100.00% | 94.10% | 90.61% | 47.18% | 0.0000% | final stats |
| MS1-41-6 | 100.00% | 94.19% | 90.69% | 46.38% | 0.0000% | final stats |
| MS1-56-1 | 100.00% | 94.05% | 90.70% | 46.04% | 0.0000% | final stats |
| MS1-56-2 | 100.00% | 94.17% | 90.72% | 46.51% | 0.0000% | final stats |
| MS1-56-3 | 100.00% | 94.70% | 91.80% | 46.41% | 0.0000% | final stats |
| MS1-56-4 | 100.00% | 95.36% | 92.56% | 46.50% | 0.0000% | final stats |
| MS1-56-5 | 100.00% | 92.66% | 88.84% | 49.44% | 0.0000% | final stats |
| MS1-56-6 | 100.00% | 94.45% | 91.09% | 46.94% | 0.0000% | final stats |
| STJM-4-1 | 100.00% | 90.04% | 84.28% | 50.21% | 0.0000% | final stats |
| STJM-4-2 | 100.00% | 93.27% | 89.48% | 47.37% | 0.0000% | final stats |
| STJM-4-3 | 100.00% | 92.42% | 87.08% | 46.87% | 0.0000% | final stats |
| STJM-4-4 | 100.00% | 94.28% | 90.76% | 47.31% | 0.0000% | final stats |
| STJM-4-5 | 100.00% | 91.91% | 86.87% | 47.89% | 0.0000% | final stats |
| STJM-4-6 | 100.00% | 93.30% | 88.29% | 47.82% | 0.0000% | final stats |
Read Lengths: Paired End
Distribution of read lengths for each sample.
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Base by Cycle: Paired End
Provides a measure of the uniformity of a distribution. The higher the average is at a certain position, the more unequal the base pair composition. N's are excluded from this calculation.
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Quality by Cycle: Paired End
Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.
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